From 84f8966fe75fb9e7eb4aae2382a5e60530152383 Mon Sep 17 00:00:00 2001 From: Lan Le Date: Wed, 8 May 2024 11:45:16 +0200 Subject: [PATCH] update dependencies - Werkzeug to 3.0.3 - gunicorn to 22.0.0 - Pillow to 10.3.0 - Jinja2 to 3.1.4 - idna to 3.7 - atomicwrites to 1.4.1 - attrs to 23.2.0 - certifi to 2024.2.2 - chardet to 5.2.0 - Click to 8.1.7 - coverage to 7.5.1 - cycler to 0.12.1 - flake8 to 3.7.9 --- .github/workflows/unit_test.yml | 2 +- README.md | 3 ++ environment.yml | 66 ++++++++++++++++----------------- requirements.txt | 26 ++++++------- 4 files changed, 50 insertions(+), 47 deletions(-) diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index e160573f..fe63855c 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -1,4 +1,4 @@ -name: Test with pytest +name: Tests on: [push] diff --git a/README.md b/README.md index f874b77b..3b38b631 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,9 @@ This backend web service provides NMR/IR/MS processing for jcamp/RAW/mzML files. +![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg) +![Testing](https://github.com/ComPlat/chem-spectra-app/actions/workflows/unit_test.yml/badge.svg) + The frontend is provided by chem-spectra-client. ### Install diff --git a/environment.yml b/environment.yml index 60e90d33..5addf1f1 100644 --- a/environment.yml +++ b/environment.yml @@ -4,50 +4,51 @@ channels: dependencies: - _libgcc_mutex=0.1=main - _openmp_mutex=5.1=1_gnu - - ca-certificates=2023.08.22=h06a4308_0 + - ca-certificates=2024.3.11=h06a4308_0 - ld_impl_linux-64=2.38=h1181459_1 - - libffi=3.4.4=h6a678d5_0 + - libffi=3.4.4=h6a678d5_1 - libgcc-ng=11.2.0=h1234567_1 - libgomp=11.2.0=h1234567_1 - libstdcxx-ng=11.2.0=h1234567_1 - ncurses=6.4=h6a678d5_0 - - openssl=3.0.11=h7f8727e_2 - - pip=23.3=py38h06a4308_0 - - python=3.8.18=h955ad1f_0 + - openssl=3.0.13=h7f8727e_1 + - pip=24.0=py38h06a4308_0 + - python=3.8.19=h955ad1f_0 - readline=8.2=h5eee18b_0 - - setuptools=68.0.0=py38h06a4308_0 - - sqlite=3.41.2=h5eee18b_0 - - tk=8.6.12=h1ccaba5_0 - - wheel=0.41.2=py38h06a4308_0 - - xz=5.4.2=h5eee18b_0 - - zlib=1.2.13=h5eee18b_0 + - setuptools=69.5.1=py38h06a4308_0 + - sqlite=3.45.3=h5eee18b_0 + - tk=8.6.14=h39e8969_0 + - wheel=0.43.0=py38h06a4308_0 + - xz=5.4.6=h5eee18b_1 + - zlib=1.2.13=h5eee18b_1 - pip: - astroid==2.15.8 - - atomicwrites==1.3.0 - - attrs==23.1.0 - - certifi==2023.7.22 + - atomicwrites==1.4.1 + - attrs==23.2.0 + - certifi==2024.2.2 - cftime==1.6.3 - - chardet==3.0.4 + - chardet==5.2.0 - charset-normalizer==3.3.2 - - click==8.0.0 + - click==8.1.7 - contourpy==1.1.1 - - coverage==4.5.3 - - cycler==0.10.0 - - dill==0.3.7 + - coverage==7.5.1 + - coverage-badge==1.1.1 + - cycler==0.12.1 + - dill==0.3.8 - entrypoints==0.3 - - exceptiongroup==1.1.3 - - flake8==3.7.7 + - exceptiongroup==1.2.1 + - flake8==3.7.9 - flask==2.2.5 - flask-jwt-extended==4.5.2 - - fonttools==4.43.1 - - gunicorn==19.9.0 - - idna==2.7 + - fonttools==4.51.0 + - gunicorn==22.0.0 + - idna==3.7 - importlib-metadata==3.6.0 - importlib-resources==5.1.3 - iniconfig==2.0.0 - isort==5.13.2 - itsdangerous==2.0.0 - - jinja2==3.1.2 + - jinja2==3.1.4 - kiwisolver==1.4.5 - lazy-object-proxy==1.10.0 - markupsafe==2.1.2 @@ -57,13 +58,12 @@ dependencies: - netcdf4==1.5.3 - numpy==1.22.4 - olefile==0.46 - - packaging==23.2 + - packaging==24.0 - pandas==2.0.3 - pathlib2==2.3.4 - - pillow==10.0.1 - - platformdirs==4.1.0 + - pillow==10.3.0 + - platformdirs==4.2.1 - pluggy==0.12.0 - - py==1.11.0 - pycodestyle==2.5.0 - pyflakes==2.1.1 - pyjwt==2.8.0 @@ -80,11 +80,11 @@ dependencies: - scipy==1.7.3 - six==1.11.0 - tomli==2.0.1 - - tomlkit==0.12.3 - - typing-extensions==4.9.0 - - tzdata==2023.3 + - tomlkit==0.12.4 + - typing-extensions==4.11.0 + - tzdata==2024.1 - urllib3==1.26.18 - - werkzeug==3.0.1 + - werkzeug==3.0.3 - wrapt==1.16.0 - zipp==0.5.2 - -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue diff --git a/requirements.txt b/requirements.txt index 97a7b6f8..73621146 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,19 +1,19 @@ rdkit==2023.9.1 -atomicwrites==1.3.0 -attrs==23.1.0 -certifi==2023.7.22 -chardet==3.0.4 -Click==8.0 -coverage==4.5.3 -cycler==0.10.0 +atomicwrites==1.4.1 +attrs==23.2.0 +certifi==2024.2.2 +chardet==5.2.0 +Click==8.1.7 +coverage==7.5.1 +cycler==0.12.1 entrypoints==0.3 -flake8==3.7.7 +flake8==3.7.9 Flask==2.2.5 -gunicorn==19.9.0 -idna==2.7 +gunicorn==22.0.0 +idna==3.7 importlib-metadata==3.6.0 itsdangerous==2.0 -Jinja2==3.1.2 +Jinja2==3.1.4 MarkupSafe==2.1.2 matplotlib==3.7.3 mccabe==0.6.1 @@ -25,7 +25,7 @@ numpy==1.22.4 olefile==0.46 pandas==2.0.3 pathlib2==2.3.4 -Pillow==10.0.1 +Pillow==10.3.0 pluggy==0.12.0 pycodestyle==2.5.0 pyflakes==2.1.1 @@ -39,7 +39,7 @@ requests==2.31.0 scipy==1.7.3 six==1.11.0 urllib3==1.26.18 -Werkzeug==3.0.1 +Werkzeug==3.0.3 zipp==0.5.2 pyopenms==2.6.0 PyJWT==2.8.0